EHV-1 Canonic Transcript dynamics (TSS ~ TES)
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic Transcript dynamics (TSS ~ TES)
Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)
When counting with either adapters, the clustering grouped ORF64 together with two late genes
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.79)... Done.## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.2)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 2: 1 ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 3: 1 ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 4: 1 ORF9 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 5: 1 ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 6: 1 ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 7: 1 ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 8: 1 ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 9: 1 ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10: 1 ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11: 1 ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12: 1 ORF37 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13: 1 ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14: 1 ORF49 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15: 1 ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16: 1 ORF51 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17: 1 ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18: 1 ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19: 1 ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20: 1 NOIR_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 21: 1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 22: 1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 23: 1 ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 24: 1 NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 25: 2 ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26: 2 ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27: 2 ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28: 2 ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29: 2 ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30: 2 ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31: 2 ORF22 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32: 2 ORF23 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33: 2 ORF24 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 34: 2 ORF25 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 35: 2 ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 36: 2 ORF27 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 37: 2 ORF28 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 38: 2 ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 39: 2 ORF32 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 40: 2 ORF33 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 41: 2 ORF35.5 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 42: 2 ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 43: 2 ORF39 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 44: 2 CTO 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 45: 2 ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 46: 2 ORF42 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 47: 2 ORF43 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 48: 2 ORF44 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 49: 2 ORF46 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 50: 2 ORF58 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 51: 2 ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 52: 2 ORF62 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 53: 2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 54: 2 ORF68 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 55: 2 ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 56: 2 ORF74 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 57: 2 ORF75 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 58: 2 ORF76 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 59: 3 ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 60: 4 ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 61: 4 ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 62: 4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 63: 4 ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 64: 5 ORF12 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 65: 5 ORF13 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 66: 5 ORF15 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 67: 5 ORF16 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 68: 5 ORF35 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 69: 5 ORF41 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 70: 5 ORF48 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 71: 5 ORF52 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 72: 5 ORF54 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 73: 5 ORF57 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 74: 5 ORF60 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 75: 5 ORF71 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 76: 5 ORF72 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.001626964 -3.0659483 0.9195982 0.57648065
## 2: 0.001626964 -3.0659483 0.9195982 0.57648065
## 3: 0.001626964 -3.0659483 0.9195982 0.57648065
## 4: 0.001626964 -3.0659483 0.9195982 0.57648065
## 5: 0.001626964 -3.0659483 0.9195982 0.57648065
## 6: 0.001626964 -3.0659483 0.9195982 0.57648065
## 7: 0.001626964 -3.0659483 0.9195982 0.57648065
## 8: 0.001626964 -3.0659483 0.9195982 0.57648065
## 9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001626964 -3.0659483 0.9195982 0.57648065
## 21: 0.001626964 -3.0659483 0.9195982 0.57648065
## 22: 0.001626964 -3.0659483 0.9195982 0.57648065
## 23: 0.001626964 -3.0659483 0.9195982 0.57648065
## 24: 0.001626964 -3.0659483 0.9195982 0.57648065
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.001864476 -3.0095246 0.9788818 0.61510585
## 34: 0.001864476 -3.0095246 0.9788818 0.61510585
## 35: 0.001864476 -3.0095246 0.9788818 0.61510585
## 36: 0.001864476 -3.0095246 0.9788818 0.61510585
## 37: 0.001864476 -3.0095246 0.9788818 0.61510585
## 38: 0.001864476 -3.0095246 0.9788818 0.61510585
## 39: 0.001864476 -3.0095246 0.9788818 0.61510585
## 40: 0.001864476 -3.0095246 0.9788818 0.61510585
## 41: 0.001864476 -3.0095246 0.9788818 0.61510585
## 42: 0.001864476 -3.0095246 0.9788818 0.61510585
## 43: 0.001864476 -3.0095246 0.9788818 0.61510585
## 44: 0.001864476 -3.0095246 0.9788818 0.61510585
## 45: 0.001864476 -3.0095246 0.9788818 0.61510585
## 46: 0.001864476 -3.0095246 0.9788818 0.61510585
## 47: 0.001864476 -3.0095246 0.9788818 0.61510585
## 48: 0.001864476 -3.0095246 0.9788818 0.61510585
## 49: 0.001864476 -3.0095246 0.9788818 0.61510585
## 50: 0.001864476 -3.0095246 0.9788818 0.61510585
## 51: 0.001864476 -3.0095246 0.9788818 0.61510585
## 52: 0.001864476 -3.0095246 0.9788818 0.61510585
## 53: 0.001864476 -3.0095246 0.9788818 0.61510585
## 54: 0.001864476 -3.0095246 0.9788818 0.61510585
## 55: 0.001864476 -3.0095246 0.9788818 0.61510585
## 56: 0.001864476 -3.0095246 0.9788818 0.61510585
## 57: 0.001864476 -3.0095246 0.9788818 0.61510585
## 58: 0.001864476 -3.0095246 0.9788818 0.61510585
## 59: 0.003563035 -2.1172717 0.8723685 0.47463144
## 60: 0.001370130 -3.1781458 0.9289840 0.55960768
## 61: 0.001370130 -3.1781458 0.9289840 0.55960768
## 62: 0.001370130 -3.1781458 0.9289840 0.55960768
## 63: 0.001370130 -3.1781458 0.9289840 0.55960768
## 64: 0.005277101 -0.7191323 0.5947468 0.03730409
## 65: 0.005277101 -0.7191323 0.5947468 0.03730409
## 66: 0.005277101 -0.7191323 0.5947468 0.03730409
## 67: 0.005277101 -0.7191323 0.5947468 0.03730409
## 68: 0.005277101 -0.7191323 0.5947468 0.03730409
## 69: 0.005277101 -0.7191323 0.5947468 0.03730409
## 70: 0.005277101 -0.7191323 0.5947468 0.03730409
## 71: 0.005277101 -0.7191323 0.5947468 0.03730409
## 72: 0.005277101 -0.7191323 0.5947468 0.03730409
## 73: 0.005277101 -0.7191323 0.5947468 0.03730409
## 74: 0.005277101 -0.7191323 0.5947468 0.03730409
## 75: 0.005277101 -0.7191323 0.5947468 0.03730409
## 76: 0.005277101 -0.7191323 0.5947468 0.03730409
## se.bp v c pchi
## [1] "ORF37" "ORF49" "ORF58" "ORF27" "ORF42" "ORF33" "ORF62"## [1] 7## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"## [1] 13Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 2: 1 ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 3: 1 ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 4: 1 ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 5: 1 ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 6: 1 ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 7: 1 ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 8: 1 ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 9: 1 ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10: 1 ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11: 1 ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12: 1 ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13: 1 ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14: 1 ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15: 1 ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16: 1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17: 1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18: 1 ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19: 1 NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20: 2 ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21: 2 ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22: 2 ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23: 2 ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24: 2 ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25: 2 ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26: 2 ORF22 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27: 2 ORF23 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28: 2 ORF24 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29: 2 ORF25 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30: 2 ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31: 2 ORF27 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32: 2 ORF28 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33: 2 ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 34: 2 ORF32 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 35: 2 ORF33 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 36: 2 ORF35.5 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 37: 2 ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 38: 2 ORF39 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 39: 2 CTO 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 40: 2 ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 41: 2 ORF42 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 42: 2 ORF43 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 43: 2 ORF44 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 44: 2 ORF46 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 45: 2 ORF58 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 46: 2 ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 47: 2 ORF62 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 48: 2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 49: 2 ORF68 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 50: 2 ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 51: 2 ORF74 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 52: 2 ORF75 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 53: 2 ORF76 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 54: 3 ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 55: 4 ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 56: 4 ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 57: 4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 58: 4 ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 59: 5 ORF9 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 60: 5 ORF37 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 61: 5 ORF49 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 62: 5 ORF51 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 63: 5 NOIR_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 64: 6 ORF12 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 65: 6 ORF13 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 66: 6 ORF15 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 67: 6 ORF16 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 68: 6 ORF35 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 69: 6 ORF41 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 70: 6 ORF48 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 71: 6 ORF52 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 72: 6 ORF54 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 73: 6 ORF57 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 74: 6 ORF60 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 75: 6 ORF71 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 76: 6 ORF72 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.001626964 -3.0659483 0.9195982 0.57648065
## 2: 0.001626964 -3.0659483 0.9195982 0.57648065
## 3: 0.001626964 -3.0659483 0.9195982 0.57648065
## 4: 0.001626964 -3.0659483 0.9195982 0.57648065
## 5: 0.001626964 -3.0659483 0.9195982 0.57648065
## 6: 0.001626964 -3.0659483 0.9195982 0.57648065
## 7: 0.001626964 -3.0659483 0.9195982 0.57648065
## 8: 0.001626964 -3.0659483 0.9195982 0.57648065
## 9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.001864476 -3.0095246 0.9788818 0.61510585
## 34: 0.001864476 -3.0095246 0.9788818 0.61510585
## 35: 0.001864476 -3.0095246 0.9788818 0.61510585
## 36: 0.001864476 -3.0095246 0.9788818 0.61510585
## 37: 0.001864476 -3.0095246 0.9788818 0.61510585
## 38: 0.001864476 -3.0095246 0.9788818 0.61510585
## 39: 0.001864476 -3.0095246 0.9788818 0.61510585
## 40: 0.001864476 -3.0095246 0.9788818 0.61510585
## 41: 0.001864476 -3.0095246 0.9788818 0.61510585
## 42: 0.001864476 -3.0095246 0.9788818 0.61510585
## 43: 0.001864476 -3.0095246 0.9788818 0.61510585
## 44: 0.001864476 -3.0095246 0.9788818 0.61510585
## 45: 0.001864476 -3.0095246 0.9788818 0.61510585
## 46: 0.001864476 -3.0095246 0.9788818 0.61510585
## 47: 0.001864476 -3.0095246 0.9788818 0.61510585
## 48: 0.001864476 -3.0095246 0.9788818 0.61510585
## 49: 0.001864476 -3.0095246 0.9788818 0.61510585
## 50: 0.001864476 -3.0095246 0.9788818 0.61510585
## 51: 0.001864476 -3.0095246 0.9788818 0.61510585
## 52: 0.001864476 -3.0095246 0.9788818 0.61510585
## 53: 0.001864476 -3.0095246 0.9788818 0.61510585
## 54: 0.003563035 -2.1172717 0.8723685 0.47463144
## 55: 0.001370130 -3.1781458 0.9289840 0.55960768
## 56: 0.001370130 -3.1781458 0.9289840 0.55960768
## 57: 0.001370130 -3.1781458 0.9289840 0.55960768
## 58: 0.001370130 -3.1781458 0.9289840 0.55960768
## 59: 0.005277101 -0.7191323 0.5947468 0.03730409
## 60: 0.005277101 -0.7191323 0.5947468 0.03730409
## 61: 0.005277101 -0.7191323 0.5947468 0.03730409
## 62: 0.005277101 -0.7191323 0.5947468 0.03730409
## 63: 0.005277101 -0.7191323 0.5947468 0.03730409
## 64: 0.005289339 -1.7163469 1.3494170 0.51125155
## 65: 0.005289339 -1.7163469 1.3494170 0.51125155
## 66: 0.005289339 -1.7163469 1.3494170 0.51125155
## 67: 0.005289339 -1.7163469 1.3494170 0.51125155
## 68: 0.005289339 -1.7163469 1.3494170 0.51125155
## 69: 0.005289339 -1.7163469 1.3494170 0.51125155
## 70: 0.005289339 -1.7163469 1.3494170 0.51125155
## 71: 0.005289339 -1.7163469 1.3494170 0.51125155
## 72: 0.005289339 -1.7163469 1.3494170 0.51125155
## 73: 0.005289339 -1.7163469 1.3494170 0.51125155
## 74: 0.005289339 -1.7163469 1.3494170 0.51125155
## 75: 0.005289339 -1.7163469 1.3494170 0.51125155
## 76: 0.005289339 -1.7163469 1.3494170 0.51125155
## se.bp v c pchi
## [1] "ORF38" "ORF58" "ORF27" "ORF42" "ORF33" "ORF62" "ORF49"## [1] 7## [1] "ORF9" "ORF37" "ORF49" "ORF51" "NOIR_1"## [1] 5Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 2: 1 ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 3: 1 ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 4: 1 ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 5: 1 ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 6: 1 ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 7: 1 ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 8: 1 ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 9: 1 ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10: 1 ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11: 1 ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12: 1 ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13: 1 ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14: 1 ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15: 1 ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16: 1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17: 1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18: 1 ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19: 1 NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20: 2 ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21: 2 ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22: 2 ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23: 2 ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24: 2 ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25: 2 ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26: 2 ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27: 2 ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28: 2 ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29: 2 ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30: 2 ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31: 2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32: 2 ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33: 3 ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 34: 4 ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 35: 4 ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 36: 4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 37: 4 ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 38: 5 ORF9 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 39: 5 ORF37 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 40: 5 ORF49 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 41: 5 ORF51 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 42: 5 NOIR_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 43: 6 ORF12 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 44: 6 ORF13 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 45: 6 ORF15 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 46: 6 ORF16 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 47: 6 ORF35 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 48: 6 ORF41 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 49: 6 ORF48 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 50: 6 ORF52 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 51: 6 ORF54 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 52: 6 ORF57 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 53: 6 ORF60 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 54: 6 ORF71 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 55: 6 ORF72 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 56: 7 ORF22 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 57: 7 ORF23 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 58: 7 ORF24 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 59: 7 ORF25 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 60: 7 ORF27 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 61: 7 ORF28 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 62: 7 ORF32 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 63: 7 ORF33 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 64: 7 ORF35.5 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 65: 7 ORF39 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 66: 7 CTO 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 67: 7 ORF42 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 68: 7 ORF43 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 69: 7 ORF44 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 70: 7 ORF46 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 71: 7 ORF58 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 72: 7 ORF62 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 73: 7 ORF68 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 74: 7 ORF74 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 75: 7 ORF75 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 76: 7 ORF76 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.001626964 -3.0659483 0.9195982 0.57648065
## 2: 0.001626964 -3.0659483 0.9195982 0.57648065
## 3: 0.001626964 -3.0659483 0.9195982 0.57648065
## 4: 0.001626964 -3.0659483 0.9195982 0.57648065
## 5: 0.001626964 -3.0659483 0.9195982 0.57648065
## 6: 0.001626964 -3.0659483 0.9195982 0.57648065
## 7: 0.001626964 -3.0659483 0.9195982 0.57648065
## 8: 0.001626964 -3.0659483 0.9195982 0.57648065
## 9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.003563035 -2.1172717 0.8723685 0.47463144
## 34: 0.001370130 -3.1781458 0.9289840 0.55960768
## 35: 0.001370130 -3.1781458 0.9289840 0.55960768
## 36: 0.001370130 -3.1781458 0.9289840 0.55960768
## 37: 0.001370130 -3.1781458 0.9289840 0.55960768
## 38: 0.005277101 -0.7191323 0.5947468 0.03730409
## 39: 0.005277101 -0.7191323 0.5947468 0.03730409
## 40: 0.005277101 -0.7191323 0.5947468 0.03730409
## 41: 0.005277101 -0.7191323 0.5947468 0.03730409
## 42: 0.005277101 -0.7191323 0.5947468 0.03730409
## 43: 0.005289339 -1.7163469 1.3494170 0.51125155
## 44: 0.005289339 -1.7163469 1.3494170 0.51125155
## 45: 0.005289339 -1.7163469 1.3494170 0.51125155
## 46: 0.005289339 -1.7163469 1.3494170 0.51125155
## 47: 0.005289339 -1.7163469 1.3494170 0.51125155
## 48: 0.005289339 -1.7163469 1.3494170 0.51125155
## 49: 0.005289339 -1.7163469 1.3494170 0.51125155
## 50: 0.005289339 -1.7163469 1.3494170 0.51125155
## 51: 0.005289339 -1.7163469 1.3494170 0.51125155
## 52: 0.005289339 -1.7163469 1.3494170 0.51125155
## 53: 0.005289339 -1.7163469 1.3494170 0.51125155
## 54: 0.005289339 -1.7163469 1.3494170 0.51125155
## 55: 0.005289339 -1.7163469 1.3494170 0.51125155
## 56: 0.005184396 -0.5512413 0.7915023 0.13830228
## 57: 0.005184396 -0.5512413 0.7915023 0.13830228
## 58: 0.005184396 -0.5512413 0.7915023 0.13830228
## 59: 0.005184396 -0.5512413 0.7915023 0.13830228
## 60: 0.005184396 -0.5512413 0.7915023 0.13830228
## 61: 0.005184396 -0.5512413 0.7915023 0.13830228
## 62: 0.005184396 -0.5512413 0.7915023 0.13830228
## 63: 0.005184396 -0.5512413 0.7915023 0.13830228
## 64: 0.005184396 -0.5512413 0.7915023 0.13830228
## 65: 0.005184396 -0.5512413 0.7915023 0.13830228
## 66: 0.005184396 -0.5512413 0.7915023 0.13830228
## 67: 0.005184396 -0.5512413 0.7915023 0.13830228
## 68: 0.005184396 -0.5512413 0.7915023 0.13830228
## 69: 0.005184396 -0.5512413 0.7915023 0.13830228
## 70: 0.005184396 -0.5512413 0.7915023 0.13830228
## 71: 0.005184396 -0.5512413 0.7915023 0.13830228
## 72: 0.005184396 -0.5512413 0.7915023 0.13830228
## 73: 0.005184396 -0.5512413 0.7915023 0.13830228
## 74: 0.005184396 -0.5512413 0.7915023 0.13830228
## 75: 0.005184396 -0.5512413 0.7915023 0.13830228
## 76: 0.005184396 -0.5512413 0.7915023 0.13830228
## se.bp v c pchi
## [1] "ORF38" "ORF49" "ORF75" "ORF23" "ORF74" "ORF58" "ORF27" "ORF32" "ORF42"
## [10] "ORF68" "ORF39" "ORF22" "ORF28" "ORF33" "CTO" "ORF76" "ORF62"## [1] 17## [1] "ORF9" "ORF37" "ORF49" "ORF51" "NOIR_1" "ORF22" "ORF23"
## [8] "ORF24" "ORF25" "ORF27" "ORF28" "ORF32" "ORF33" "ORF35.5"
## [15] "ORF39" "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58"
## [22] "ORF62" "ORF68" "ORF74" "ORF75" "ORF76"## [1] 26Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 2: 1 ORF5 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 3: 1 ORF7 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 4: 1 ORF10 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 5: 1 ORF17 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 6: 1 ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 7: 1 ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 8: 1 ORF30 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 9: 1 ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10: 1 ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11: 1 ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12: 1 ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 13: 1 ORF53 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 14: 1 ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 15: 1 ORF63 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 16: 1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 17: 1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 18: 1 ORF69 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 19: 1 NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 20: 2 ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21: 2 ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22: 2 ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23: 2 ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24: 2 ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25: 2 ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 26: 2 ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 27: 2 ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 28: 2 ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 29: 2 ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 30: 2 ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 31: 2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 32: 2 ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 33: 3 ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 34: 4 ORF6 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 35: 4 ORF18 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 36: 4 ORF64_1 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 37: 4 ORF70 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 38: 5 ORF9 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 39: 5 ORF37 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 40: 5 ORF51 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 41: 6 ORF12 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 42: 6 ORF13 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 43: 6 ORF15 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 44: 6 ORF16 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 45: 6 ORF35 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 46: 6 ORF41 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 47: 6 ORF48 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 48: 6 ORF52 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 49: 6 ORF54 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 50: 6 ORF57 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 51: 6 ORF60 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 52: 6 ORF71 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 53: 6 ORF72 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 54: 7 ORF22 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 55: 7 ORF23 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 56: 7 ORF25 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 57: 7 ORF28 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 58: 7 ORF33 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 59: 7 ORF35.5 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 60: 7 ORF39 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 61: 7 CTO 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 62: 7 ORF42 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 63: 7 ORF43 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 64: 7 ORF44 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 65: 7 ORF46 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 66: 7 ORF58 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 67: 7 ORF62 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 68: 7 ORF68 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 69: 7 ORF75 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 70: 8 ORF24 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 71: 8 ORF74 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 72: 8 ORF76 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 73: 9 ORF27 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 74: 9 ORF32 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 75: 10 ORF49 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 76: 10 NOIR_1 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.001626964 -3.0659483 0.9195982 0.57648065
## 2: 0.001626964 -3.0659483 0.9195982 0.57648065
## 3: 0.001626964 -3.0659483 0.9195982 0.57648065
## 4: 0.001626964 -3.0659483 0.9195982 0.57648065
## 5: 0.001626964 -3.0659483 0.9195982 0.57648065
## 6: 0.001626964 -3.0659483 0.9195982 0.57648065
## 7: 0.001626964 -3.0659483 0.9195982 0.57648065
## 8: 0.001626964 -3.0659483 0.9195982 0.57648065
## 9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001626964 -3.0659483 0.9195982 0.57648065
## 13: 0.001626964 -3.0659483 0.9195982 0.57648065
## 14: 0.001626964 -3.0659483 0.9195982 0.57648065
## 15: 0.001626964 -3.0659483 0.9195982 0.57648065
## 16: 0.001626964 -3.0659483 0.9195982 0.57648065
## 17: 0.001626964 -3.0659483 0.9195982 0.57648065
## 18: 0.001626964 -3.0659483 0.9195982 0.57648065
## 19: 0.001626964 -3.0659483 0.9195982 0.57648065
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.001864476 -3.0095246 0.9788818 0.61510585
## 26: 0.001864476 -3.0095246 0.9788818 0.61510585
## 27: 0.001864476 -3.0095246 0.9788818 0.61510585
## 28: 0.001864476 -3.0095246 0.9788818 0.61510585
## 29: 0.001864476 -3.0095246 0.9788818 0.61510585
## 30: 0.001864476 -3.0095246 0.9788818 0.61510585
## 31: 0.001864476 -3.0095246 0.9788818 0.61510585
## 32: 0.001864476 -3.0095246 0.9788818 0.61510585
## 33: 0.003563035 -2.1172717 0.8723685 0.47463144
## 34: 0.001370130 -3.1781458 0.9289840 0.55960768
## 35: 0.001370130 -3.1781458 0.9289840 0.55960768
## 36: 0.001370130 -3.1781458 0.9289840 0.55960768
## 37: 0.001370130 -3.1781458 0.9289840 0.55960768
## 38: 0.005277101 -0.7191323 0.5947468 0.03730409
## 39: 0.005277101 -0.7191323 0.5947468 0.03730409
## 40: 0.005277101 -0.7191323 0.5947468 0.03730409
## 41: 0.005289339 -1.7163469 1.3494170 0.51125155
## 42: 0.005289339 -1.7163469 1.3494170 0.51125155
## 43: 0.005289339 -1.7163469 1.3494170 0.51125155
## 44: 0.005289339 -1.7163469 1.3494170 0.51125155
## 45: 0.005289339 -1.7163469 1.3494170 0.51125155
## 46: 0.005289339 -1.7163469 1.3494170 0.51125155
## 47: 0.005289339 -1.7163469 1.3494170 0.51125155
## 48: 0.005289339 -1.7163469 1.3494170 0.51125155
## 49: 0.005289339 -1.7163469 1.3494170 0.51125155
## 50: 0.005289339 -1.7163469 1.3494170 0.51125155
## 51: 0.005289339 -1.7163469 1.3494170 0.51125155
## 52: 0.005289339 -1.7163469 1.3494170 0.51125155
## 53: 0.005289339 -1.7163469 1.3494170 0.51125155
## 54: 0.005184396 -0.5512413 0.7915023 0.13830228
## 55: 0.005184396 -0.5512413 0.7915023 0.13830228
## 56: 0.005184396 -0.5512413 0.7915023 0.13830228
## 57: 0.005184396 -0.5512413 0.7915023 0.13830228
## 58: 0.005184396 -0.5512413 0.7915023 0.13830228
## 59: 0.005184396 -0.5512413 0.7915023 0.13830228
## 60: 0.005184396 -0.5512413 0.7915023 0.13830228
## 61: 0.005184396 -0.5512413 0.7915023 0.13830228
## 62: 0.005184396 -0.5512413 0.7915023 0.13830228
## 63: 0.005184396 -0.5512413 0.7915023 0.13830228
## 64: 0.005184396 -0.5512413 0.7915023 0.13830228
## 65: 0.005184396 -0.5512413 0.7915023 0.13830228
## 66: 0.005184396 -0.5512413 0.7915023 0.13830228
## 67: 0.005184396 -0.5512413 0.7915023 0.13830228
## 68: 0.005184396 -0.5512413 0.7915023 0.13830228
## 69: 0.005184396 -0.5512413 0.7915023 0.13830228
## 70: 0.005314391 -0.9727072 0.8743440 0.26787994
## 71: 0.005314391 -0.9727072 0.8743440 0.26787994
## 72: 0.005314391 -0.9727072 0.8743440 0.26787994
## 73: 0.005288858 -0.8567880 0.7295011 0.03771967
## 74: 0.005288858 -0.8567880 0.7295011 0.03771967
## 75: 0.005328329 -0.9683955 0.9780811 0.28653102
## 76: 0.005328329 -0.9683955 0.9780811 0.28653102
## se.bp v c pchi
## [1] "ORF38" "ORF62" "ORF28" "ORF68" "ORF76" "ORF49"## [1] 6## [1] "ORF9" "ORF37" "ORF51" "ORF22" "ORF23" "ORF25" "ORF28"
## [8] "ORF33" "ORF35.5" "ORF39" "CTO" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF58" "ORF62" "ORF68" "ORF75" "ORF27" "ORF32"## [1] 21Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 2: 1 ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 3: 1 ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 4: 1 ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 5: 1 ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 6: 1 ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 7: 1 ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 8: 1 ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 9: 1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10: 1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11: 1 NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12: 2 ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 13: 2 ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 14: 2 ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 15: 2 ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 16: 2 ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 17: 2 ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 18: 2 ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 19: 2 ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 20: 2 ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21: 2 ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22: 2 ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23: 2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24: 2 ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25: 3 ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 26: 4 ORF5 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 27: 4 ORF7 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 28: 4 ORF10 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 29: 4 ORF17 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 30: 4 ORF30 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 31: 4 ORF53 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 32: 4 ORF63 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 33: 4 ORF69 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 34: 5 ORF6 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 35: 5 ORF18 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 36: 5 ORF64_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 37: 6 ORF9 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 38: 6 ORF37 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 39: 6 ORF51 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 40: 7 ORF12 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 41: 7 ORF13 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 42: 7 ORF15 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 43: 7 ORF16 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 44: 7 ORF35 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 45: 7 ORF41 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 46: 7 ORF48 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 47: 7 ORF52 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 48: 7 ORF54 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 49: 7 ORF57 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 50: 7 ORF60 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 51: 7 ORF71 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 52: 7 ORF72 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 53: 8 ORF22 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 54: 8 ORF23 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 55: 8 ORF25 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 56: 8 ORF28 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 57: 8 ORF33 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 58: 8 ORF35.5 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 59: 8 ORF39 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 60: 8 CTO 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 61: 8 ORF42 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 62: 8 ORF43 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 63: 8 ORF44 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 64: 8 ORF46 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 65: 8 ORF58 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 66: 8 ORF62 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 67: 8 ORF68 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 68: 8 ORF75 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 69: 9 ORF24 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 70: 9 ORF74 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 71: 9 ORF76 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 72: 10 ORF27 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 73: 10 ORF32 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 74: 11 ORF49 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 75: 11 NOIR_1 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 76: 12 ORF70 0.9815714 0.9979697 0.6635465 3.593511e-03 5.276070e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.001626964 -3.0659483 0.9195982 0.57648065
## 2: 0.001626964 -3.0659483 0.9195982 0.57648065
## 3: 0.001626964 -3.0659483 0.9195982 0.57648065
## 4: 0.001626964 -3.0659483 0.9195982 0.57648065
## 5: 0.001626964 -3.0659483 0.9195982 0.57648065
## 6: 0.001626964 -3.0659483 0.9195982 0.57648065
## 7: 0.001626964 -3.0659483 0.9195982 0.57648065
## 8: 0.001626964 -3.0659483 0.9195982 0.57648065
## 9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001864476 -3.0095246 0.9788818 0.61510585
## 13: 0.001864476 -3.0095246 0.9788818 0.61510585
## 14: 0.001864476 -3.0095246 0.9788818 0.61510585
## 15: 0.001864476 -3.0095246 0.9788818 0.61510585
## 16: 0.001864476 -3.0095246 0.9788818 0.61510585
## 17: 0.001864476 -3.0095246 0.9788818 0.61510585
## 18: 0.001864476 -3.0095246 0.9788818 0.61510585
## 19: 0.001864476 -3.0095246 0.9788818 0.61510585
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.003563035 -2.1172717 0.8723685 0.47463144
## 26: 0.001370130 -3.1781458 0.9289840 0.55960768
## 27: 0.001370130 -3.1781458 0.9289840 0.55960768
## 28: 0.001370130 -3.1781458 0.9289840 0.55960768
## 29: 0.001370130 -3.1781458 0.9289840 0.55960768
## 30: 0.001370130 -3.1781458 0.9289840 0.55960768
## 31: 0.001370130 -3.1781458 0.9289840 0.55960768
## 32: 0.001370130 -3.1781458 0.9289840 0.55960768
## 33: 0.001370130 -3.1781458 0.9289840 0.55960768
## 34: 0.005277101 -0.7191323 0.5947468 0.03730409
## 35: 0.005277101 -0.7191323 0.5947468 0.03730409
## 36: 0.005277101 -0.7191323 0.5947468 0.03730409
## 37: 0.005289339 -1.7163469 1.3494170 0.51125155
## 38: 0.005289339 -1.7163469 1.3494170 0.51125155
## 39: 0.005289339 -1.7163469 1.3494170 0.51125155
## 40: 0.005184396 -0.5512413 0.7915023 0.13830228
## 41: 0.005184396 -0.5512413 0.7915023 0.13830228
## 42: 0.005184396 -0.5512413 0.7915023 0.13830228
## 43: 0.005184396 -0.5512413 0.7915023 0.13830228
## 44: 0.005184396 -0.5512413 0.7915023 0.13830228
## 45: 0.005184396 -0.5512413 0.7915023 0.13830228
## 46: 0.005184396 -0.5512413 0.7915023 0.13830228
## 47: 0.005184396 -0.5512413 0.7915023 0.13830228
## 48: 0.005184396 -0.5512413 0.7915023 0.13830228
## 49: 0.005184396 -0.5512413 0.7915023 0.13830228
## 50: 0.005184396 -0.5512413 0.7915023 0.13830228
## 51: 0.005184396 -0.5512413 0.7915023 0.13830228
## 52: 0.005184396 -0.5512413 0.7915023 0.13830228
## 53: 0.005314391 -0.9727072 0.8743440 0.26787994
## 54: 0.005314391 -0.9727072 0.8743440 0.26787994
## 55: 0.005314391 -0.9727072 0.8743440 0.26787994
## 56: 0.005314391 -0.9727072 0.8743440 0.26787994
## 57: 0.005314391 -0.9727072 0.8743440 0.26787994
## 58: 0.005314391 -0.9727072 0.8743440 0.26787994
## 59: 0.005314391 -0.9727072 0.8743440 0.26787994
## 60: 0.005314391 -0.9727072 0.8743440 0.26787994
## 61: 0.005314391 -0.9727072 0.8743440 0.26787994
## 62: 0.005314391 -0.9727072 0.8743440 0.26787994
## 63: 0.005314391 -0.9727072 0.8743440 0.26787994
## 64: 0.005314391 -0.9727072 0.8743440 0.26787994
## 65: 0.005314391 -0.9727072 0.8743440 0.26787994
## 66: 0.005314391 -0.9727072 0.8743440 0.26787994
## 67: 0.005314391 -0.9727072 0.8743440 0.26787994
## 68: 0.005314391 -0.9727072 0.8743440 0.26787994
## 69: 0.005288858 -0.8567880 0.7295011 0.03771967
## 70: 0.005288858 -0.8567880 0.7295011 0.03771967
## 71: 0.005288858 -0.8567880 0.7295011 0.03771967
## 72: 0.005328329 -0.9683955 0.9780811 0.28653102
## 73: 0.005328329 -0.9683955 0.9780811 0.28653102
## 74: 0.004586799 -1.5470381 0.7851831 0.39223675
## 75: 0.004586799 -1.5470381 0.7851831 0.39223675
## 76: 0.005186459 -1.6477916 1.2256298 0.38455221
## se.bp v c pchi
## [1] "ORF65_1" "ORF62" "ORF28" "ORF68" "ORF76" "ORF49"## [1] 6## [1] "ORF6" "ORF18" "ORF64_1" "ORF12" "ORF13" "ORF15" "ORF16"
## [8] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [15] "ORF71" "ORF72" "ORF24" "ORF74" "ORF76"## [1] 19Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 2: 1 ORF20 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 3: 1 ORF21 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 4: 1 ORF31 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 5: 1 ORF34 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 6: 1 ORF38 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 7: 1 ORF50 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 8: 1 ORF61 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 9: 1 ORF65_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 10: 1 ORF67_1 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 11: 1 NOIR_2 0.9998118 0.9999663 0.9840775 1.180450e-04 2.453283e-05
## 12: 2 ORF2 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 13: 2 ORF3 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 14: 2 ORF8 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 15: 2 ORF11 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 16: 2 ORF14 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 17: 2 ORF19 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 18: 2 ORF26 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 19: 2 ORF29 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 20: 2 ORF36 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 21: 2 ORF40 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 22: 2 ORF59 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 23: 2 ORF66_1 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 24: 2 ORF73 0.9997970 0.9999667 0.9788544 1.162895e-04 2.228015e-05
## 25: 3 ORF4 0.9927075 0.9986035 0.8934163 1.889334e-03 4.471760e-04
## 26: 4 ORF5 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 27: 4 ORF7 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 28: 4 ORF10 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 29: 4 ORF17 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 30: 4 ORF30 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 31: 4 ORF53 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 32: 4 ORF63 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 33: 4 ORF69 0.9998865 0.9999800 0.9877489 7.572633e-05 1.545259e-05
## 34: 5 ORF6 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 35: 5 ORF18 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 36: 5 ORF64_1 0.6578215 0.9055566 0.5494950 3.234843e-02 1.307128e-02
## 37: 6 ORF9 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 38: 6 ORF37 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 39: 6 ORF51 0.9877477 0.9989144 0.6431643 2.540233e-03 3.005063e-04
## 40: 7 ORF12 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 41: 7 ORF13 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 42: 7 ORF15 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 43: 7 ORF16 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 44: 7 ORF35 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 45: 7 ORF41 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 46: 7 ORF48 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 47: 7 ORF52 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 48: 7 ORF54 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 49: 7 ORF57 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 50: 7 ORF60 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 51: 7 ORF71 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 52: 7 ORF72 0.5815826 0.9103225 0.4050640 3.895013e-02 1.292741e-02
## 53: 8 ORF22 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 54: 8 ORF23 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 55: 8 ORF25 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 56: 8 ORF28 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 57: 8 ORF33 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 58: 8 ORF35.5 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 59: 8 ORF39 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 60: 8 CTO 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 61: 8 ORF42 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 62: 8 ORF43 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 63: 8 ORF44 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 64: 8 ORF46 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 65: 8 ORF58 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 66: 8 ORF62 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 67: 8 ORF68 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 68: 8 ORF75 0.8304936 0.9676301 0.5391780 2.107766e-02 5.733573e-03
## 69: 9 ORF24 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 70: 9 ORF74 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 71: 9 ORF76 0.7580526 0.9436631 0.5506434 2.647512e-02 8.865501e-03
## 72: 10 ORF27 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 73: 10 ORF32 0.8427069 0.9742012 0.4961361 2.032104e-02 4.792183e-03
## 74: 11 ORF49 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 75: 11 NOIR_1 0.9544600 0.9901555 0.7769267 7.867447e-03 2.211067e-03
## 76: 12 ORF70 0.9815714 0.9979697 0.6635465 3.593511e-03 5.276070e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.001626964 -3.0659483 0.9195982 0.57648065
## 2: 0.001626964 -3.0659483 0.9195982 0.57648065
## 3: 0.001626964 -3.0659483 0.9195982 0.57648065
## 4: 0.001626964 -3.0659483 0.9195982 0.57648065
## 5: 0.001626964 -3.0659483 0.9195982 0.57648065
## 6: 0.001626964 -3.0659483 0.9195982 0.57648065
## 7: 0.001626964 -3.0659483 0.9195982 0.57648065
## 8: 0.001626964 -3.0659483 0.9195982 0.57648065
## 9: 0.001626964 -3.0659483 0.9195982 0.57648065
## 10: 0.001626964 -3.0659483 0.9195982 0.57648065
## 11: 0.001626964 -3.0659483 0.9195982 0.57648065
## 12: 0.001864476 -3.0095246 0.9788818 0.61510585
## 13: 0.001864476 -3.0095246 0.9788818 0.61510585
## 14: 0.001864476 -3.0095246 0.9788818 0.61510585
## 15: 0.001864476 -3.0095246 0.9788818 0.61510585
## 16: 0.001864476 -3.0095246 0.9788818 0.61510585
## 17: 0.001864476 -3.0095246 0.9788818 0.61510585
## 18: 0.001864476 -3.0095246 0.9788818 0.61510585
## 19: 0.001864476 -3.0095246 0.9788818 0.61510585
## 20: 0.001864476 -3.0095246 0.9788818 0.61510585
## 21: 0.001864476 -3.0095246 0.9788818 0.61510585
## 22: 0.001864476 -3.0095246 0.9788818 0.61510585
## 23: 0.001864476 -3.0095246 0.9788818 0.61510585
## 24: 0.001864476 -3.0095246 0.9788818 0.61510585
## 25: 0.003563035 -2.1172717 0.8723685 0.47463144
## 26: 0.001370130 -3.1781458 0.9289840 0.55960768
## 27: 0.001370130 -3.1781458 0.9289840 0.55960768
## 28: 0.001370130 -3.1781458 0.9289840 0.55960768
## 29: 0.001370130 -3.1781458 0.9289840 0.55960768
## 30: 0.001370130 -3.1781458 0.9289840 0.55960768
## 31: 0.001370130 -3.1781458 0.9289840 0.55960768
## 32: 0.001370130 -3.1781458 0.9289840 0.55960768
## 33: 0.001370130 -3.1781458 0.9289840 0.55960768
## 34: 0.005277101 -0.7191323 0.5947468 0.03730409
## 35: 0.005277101 -0.7191323 0.5947468 0.03730409
## 36: 0.005277101 -0.7191323 0.5947468 0.03730409
## 37: 0.005289339 -1.7163469 1.3494170 0.51125155
## 38: 0.005289339 -1.7163469 1.3494170 0.51125155
## 39: 0.005289339 -1.7163469 1.3494170 0.51125155
## 40: 0.005184396 -0.5512413 0.7915023 0.13830228
## 41: 0.005184396 -0.5512413 0.7915023 0.13830228
## 42: 0.005184396 -0.5512413 0.7915023 0.13830228
## 43: 0.005184396 -0.5512413 0.7915023 0.13830228
## 44: 0.005184396 -0.5512413 0.7915023 0.13830228
## 45: 0.005184396 -0.5512413 0.7915023 0.13830228
## 46: 0.005184396 -0.5512413 0.7915023 0.13830228
## 47: 0.005184396 -0.5512413 0.7915023 0.13830228
## 48: 0.005184396 -0.5512413 0.7915023 0.13830228
## 49: 0.005184396 -0.5512413 0.7915023 0.13830228
## 50: 0.005184396 -0.5512413 0.7915023 0.13830228
## 51: 0.005184396 -0.5512413 0.7915023 0.13830228
## 52: 0.005184396 -0.5512413 0.7915023 0.13830228
## 53: 0.005314391 -0.9727072 0.8743440 0.26787994
## 54: 0.005314391 -0.9727072 0.8743440 0.26787994
## 55: 0.005314391 -0.9727072 0.8743440 0.26787994
## 56: 0.005314391 -0.9727072 0.8743440 0.26787994
## 57: 0.005314391 -0.9727072 0.8743440 0.26787994
## 58: 0.005314391 -0.9727072 0.8743440 0.26787994
## 59: 0.005314391 -0.9727072 0.8743440 0.26787994
## 60: 0.005314391 -0.9727072 0.8743440 0.26787994
## 61: 0.005314391 -0.9727072 0.8743440 0.26787994
## 62: 0.005314391 -0.9727072 0.8743440 0.26787994
## 63: 0.005314391 -0.9727072 0.8743440 0.26787994
## 64: 0.005314391 -0.9727072 0.8743440 0.26787994
## 65: 0.005314391 -0.9727072 0.8743440 0.26787994
## 66: 0.005314391 -0.9727072 0.8743440 0.26787994
## 67: 0.005314391 -0.9727072 0.8743440 0.26787994
## 68: 0.005314391 -0.9727072 0.8743440 0.26787994
## 69: 0.005288858 -0.8567880 0.7295011 0.03771967
## 70: 0.005288858 -0.8567880 0.7295011 0.03771967
## 71: 0.005288858 -0.8567880 0.7295011 0.03771967
## 72: 0.005328329 -0.9683955 0.9780811 0.28653102
## 73: 0.005328329 -0.9683955 0.9780811 0.28653102
## 74: 0.004586799 -1.5470381 0.7851831 0.39223675
## 75: 0.004586799 -1.5470381 0.7851831 0.39223675
## 76: 0.005186459 -1.6477916 1.2256298 0.38455221
## se.bp v c pchi
## [1] "ORF65_1" "ORF62" "ORF28" "ORF68" "ORF76" "ORF49"## [1] 6## [1] "ORF6" "ORF18" "ORF64_1" "ORF12" "ORF13" "ORF15" "ORF16"
## [8] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [15] "ORF71" "ORF72" "ORF24" "ORF74" "ORF76"## [1] 19Remove genes from clusters ?
## [1] "ORF6" "ORF18" "ORF64_1" "ORF12" "ORF13" "ORF15" "ORF16"
## [8] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [15] "ORF71" "ORF72" "ORF24" "ORF74" "ORF76"## [1] 19## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 8 16
## 2: 2 13
## 3: 7 13
## 4: 1 11
## 5: 4 8
## 6: 5 3
## 7: 6 3
## 8: 9 3
## 9: 10 2
## 10: 11 2
## 11: 3 1
## 12: 12 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
